R4RNA: An R package for RNA visualization and analysis
Version 1.4.0

A package for RNA basepair analysis, including the visualization of basepairs as arc diagrams for easy comparison and annotation of sequence and structure. Arc diagrams can additionally be projected onto multiple sequence alignments to assess basepair conservation and covariation, with numerical methods for computing statistics for each.

AuthorDaniel Lai, Irmtraud Meyer <irmtraud.meyer@cantab.net>
Bioconductor views Alignment DataImport DataRepresentation MultipleComparison MultipleSequenceAlignment Preprocessing Visualization
Date of publicationNone
MaintainerDaniel Lai <jujubix@cs.ubc.ca>
LicenseGPL-3
Version1.4.0
URL http://www.e-rna.org/r-chie/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("R4RNA")

Getting started

Package overview

Popular man pages

basepairFrequency: Calculates the frequency of each basepair
helix: Helices predicted by TRANSAT with p-values
logicalHelix: Logical filters of helix by type
logseq: Log base 10 sequence, floor and ceiling
R4RNA-package: An R package for RNA visualization and analysis
readStructure: Read secondary structure file
structureMismatchScore: Scores how a basepair structure fits a sequence
See all...

All man pages Function index File listing

Man pages

alignmentStatistics: Compute statistics for a multiple sequence alignments
as.helix: Coerce to a Helix Data Frame
basepairFrequency: Calculates the frequency of each basepair
blankPlot: Create a blank plotting canvas
colourHelices: Assign colours to helices
expandCollapseHelix: Expand or collapse helices to and from basepairs
helix: Helices predicted by TRANSAT with p-values
logicalHelix: Logical filters of helix by type
logseq: Log base 10 sequence, floor and ceiling
plotCovariance: Plot nucleotide sequence coloured by covariance
plotHelix: Plots helices in arc diagram
R4RNA-package: An R package for RNA visualization and analysis
readStructure: Read secondary structure file
structureMismatchScore: Scores how a basepair structure fits a sequence
unknottedGroups: Partition basepairs into unknotted groups
viennaToHelix: Convert helix structures to and from other formats
writeHelix: Write out a helix data frame into a text file

Functions

R4RNA Man page
R4RNA-package Man page
alignmentCanonical Man page Source code
alignmentConservation Man page Source code
alignmentCovariation Man page Source code
alignmentPercentGaps Man page Source code
anglesArc Source code
arc Source code
as.helix Man page Source code
baseConservation Man page Source code
basepairCanonical Man page Source code
basepairConservation Man page Source code
basepairCovariation Man page Source code
basepairFrequency Man page Source code
blankPlot Man page Source code
collapseHelix Man page Source code
colourBy.internal Source code
colourByBasepairFrequency Man page Source code
colourByCanonical Man page Source code
colourByConservation Man page Source code
colourByCount Man page Source code
colourByCovariation Man page Source code
colourByUnknottedGroups Man page Source code
colourByValue Man page Source code
columnPercentIdentity Source code
defaultPalette Man page Source code
emptyHelix Source code
expandHelix Man page Source code
expandNumberedHelix Source code
fasta Man page
getBaseColours Source code
getCovarianceColours Source code
getSequenceColour Source code
hamming Source code
helix Man page
helixCanonical Man page Source code
helixConservation Man page Source code
helixCovariation Man page Source code
helixToBpseq Man page Source code
helixToConnect Man page Source code
helixToVienna Man page Source code
is.helix Man page Source code
isConflictingHelix Man page Source code
isDuplicatingHelix Man page Source code
isOverlappingHelix Man page Source code
isValidBp Source code
is_pseudoknotted Source code
known Man page
logceiling Man page Source code
logfloor Man page Source code
logseq Man page Source code
maxHeight Man page Source code
openFileOrConnection Source code
parseBracket Man page
plotArc Man page Source code
plotArcs Man page Source code
plotArrow Source code
plotCovariance Man page Source code
plotCovarianceGrid Source code
plotCovarianceLine Source code
plotCovarianceSpecies Source code
plotCovarianceText Source code
plotDoubleCovariance Man page Source code
plotDoubleHelix Man page Source code
plotHelix Man page Source code
plotOverlapCovariance Man page Source code
plotOverlapHelix Man page Source code
plotScale Source code
readBpseq Man page Source code
readConnect Man page Source code
readHelix Man page Source code
readVienna Man page Source code
structureMismatchScore Man page Source code
structureMismatchScoreInternal Source code
unknottedGroups Man page Source code
viennaToHelix Man page Source code
writeHelix Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/io.R
R/misc.R
R/plot.R
R/stats.R
build
build/vignette.rds
data
data/helix.RData
inst
inst/CITATION
inst/doc
inst/doc/R4RNA.R
inst/doc/R4RNA.Rnw
inst/doc/R4RNA.pdf
inst/extdata
inst/extdata/bpseq.txt
inst/extdata/connect.txt
inst/extdata/fasta.txt
inst/extdata/helix.txt
inst/extdata/vienna.txt
man
man/R4RNA-package.Rd
man/alignmentStatistics.Rd
man/as.helix.Rd
man/basepairFrequency.Rd
man/blankPlot.Rd
man/colourHelices.Rd
man/expandCollapseHelix.Rd
man/helix.Rd
man/logicalHelix.Rd
man/logseq.Rd
man/plotCovariance.Rd
man/plotHelix.Rd
man/readStructure.Rd
man/structureMismatchScore.Rd
man/unknottedGroups.Rd
man/viennaToHelix.Rd
man/writeHelix.Rd
vignettes
vignettes/R4RNA.Rnw
R4RNA documentation built on May 20, 2017, 9:56 p.m.